Patterned functionalized silicon surfaces

ABSTRACT

The present invention provides a method for preparing a silicon substrate and a silicon substrate having a silicon surface comprising a pattern of covalently bound monolayers. Each of the monolayers comprises an alkyne, wherein at least a portion of each monolayer is no more than about 5 molecules of the alkyne wide.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.10/887,792, filed Jul. 9, 2004, which claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application Ser. No. 60/486,571, filed Jul.11, 2003, which is expressly incorporated herein by reference.

GOVERNMENT RIGHTS

Research relating to this invention was supported in part by the U.S.Government under Grants Nos. CHE-0110846 and CHE-9875150 awarded fromthe National Science Foundation. The U.S. Government may have certainrights in this invention.

BACKGROUND

Silicon surface chemistry is of fundamental technical significancebecause of the ubiquitous role of silicon in modern technology; yetsilicon/organic chemistry is only just beginning to be investigated.Virtually all microprocessor chips in electronic products are based uponcrystalline silicon wafers. Control of silicon surface chemistry iscrucial to allow access to technologically functional thin films forfabrication of new electronic devices. In 1990, Canham and co-workersshowed that silicon wafers could be etched using hydrofluoric acid toproduce a porous layer that is only a few microns thick (termed poroussilicon) and exhibits photoluminescence upon exposure to UV light(Canham, L. T. Appl. Phys. Lett. 1990, 57, 1046). The surface of poroussilicon (Si) is populated with metastable Si—H_(x) bonds (x=1,2,3),exposed Si—Si bonds, and defects such as open valence, “dangling” Siatoms. Potential applications for porous silicon include uses aschemical sensors, biosensors, optoelectronic devices such aselectroluminescent displays, photodetectors, mass spectrometry(desorption ionization on silicon or DIOS), interfacing with neurons andother nerve cells, and as a matrix for photopumped tunable lasers. As aresult, modification and characterization of photoluminescent poroussilicon surfaces has become an area of intense interest.

Recent developments in the functionalization of porous silicon haveenabled Si—C bonds to be formed on the porous-Si surface by attackingthe weak Si—Si bonds of exposed nanocrystalline submaterial withGrignard or alkyllithium reagents. Grignard and alkyllithiumtransmetallation and the use of Lewis acid catalysis have also been usedto exploit the great population of surface Si—H bonds. Thermal,radical-mediated, and UV photolytic alkene hydrosilylation has also beenreported for flat Si and Si hydride surfaces. In general, chemistry thatworks on porous silicon also applies to flat Si (100) and Si (111)surfaces based on substantial literature precedent. Additionally, usingthe Si surface as a semiconducting electrode, several workers haverecently reported electrochemical Si—C bond formation by directgrafting, an approach with few parallels to soluble, molecular silanechemistry. U.S. patent application Ser. No. 09/716,614, hereinincorporated by reference, teaches a method of functionalizing the Sisurfaces by electrochemically grafting terminal alkynes to siliconresulting in two distinct surface derivations depending on the polarityof the surface bias. Cathodic electrografting (CEG) directly attachesalkynes to the surface, whereas anodic electrografting (AEG) of alkynesyields an alkyl surface.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Representative surfaces prepared by CEG of alkynes to poroussilicon. The numbers refer to 1) phenylacetylene, 2) 1-dodecyne, 3)1-pentyne, 4) 1,7-octadiyne, 5) p-Br-phenylacetylene, 6)1,4-diethynylbenzene, and 7) diphenylphosphinoacetylene. The percentagebelow each surface represents the % photoluminescence remaining afterfunctionalization by CEG.

FIG. 2. CEG of 1-dodecyne.

FIG. 3. CEG of 1,7-octadiyne.

FIG. 4. CEG of phenylacetylene.

FIG. 5. CEG of p-Br-phenylacetylene.

FIG. 6. CEG of 1,4-diethynylbenzene.

FIG. 7. CEG of diphenylphosphinnoacetylene.

FIG. 8. AEG of 1-dodecyne.

FIG. 9. AEG of phenylacetylene.

FIG. 10. CEG of 1-dodecyne after 10 minutes of boiling in NaOH.

FIG. 11. AEG of 1-dodecyne after 10 minutes of boiling in NaOH.

FIG. 12. CEG of 1-dodecanethiol.

FIG. 13. CEG of 1-pentyne (top panel) and AEG of 1-dodecyne (bottompanel).

FIG. 14. CEG reaction carried out in the absence of alkyne.

FIG. 15. BH3.THF hydroborated 1-pentynyl.

FIG. 16. Disiamylborane hydroborated 1-trimethylsilyl-dodecyne.

FIG. 17. Disiamylborane hydroborated 1-pentynyl.

FIG. 18. Photoluminescence (PL) of freshly etched porous silicon (solidline) and 1-pentynyl (dotted line) grafted by CEG.

FIG. 19. PL of freshly etched porous silicon (solid line) and1,7-octadiyne (dotted line) grafted by CEG.

FIG. 20. PL of freshly etched porous silicon (solid line) and 1-dodecynegrafted by CEG (dotted line).

FIG. 21. PL of freshly etched porous silicon (solid line) andphenylacetylene (dotted line) grafted by CEG.

FIG. 22. PL of freshly etched porous silicon (solid line) and CEG in theabsence of alkyne (dotted line).

FIG. 23. PL of freshly etched porous silicon (solid line) and 1-dodecynegrafted by AEG (dotted line).

FIG. 24. (a) Schematic of platinum coated AFM tip coming into contactwith alkyne on a hydrophilic silicon oxide surface. (b) Alkyne coatedAFM tip coming into contact with a hydrophilic silicon hydride surface.(c) Reductive coupling reaction between surface Si—H groups and thealkyne.

FIG. 25. (a) Schematic of the cathodic electrografting (CEG) experimentto be carried out with CP-AFM. (b) Application of a negative bias to thesemiconducting surface [tip(+)] drives the reductive coupling reactionbetween surface Si—H groups and the alkyne. (c) Nanolithography iscarried out by ‘writing’ with the tip, leaving covalently bound alkynylfunctionalities on the surface. (d) Different areas of the surface maybe patterned with dissimilar alkynes, allowing for spatially definedarrays of varying functionalities, such as the interdigitated patternshown.

FIG. 26. (a) Tapping mode height image of dodecyne. (b) Tapping modephase image of dodecyne. (c) Topographical height information ofdodecyne.

FIG. 27. (a) Tapping mode microscopy height image of 1,4diethynylbenzene. (b) Phase image of 1,4 diethynylbenzene. (c)Topographical height image of 1,4 diethynylbenzene.

FIG. 28. (a) Tapping mode height image of octadecyne. (b) Phase modeimage of octadecyne. (c) Topographical information of octadecyne.

FIG. 29. (a) Tapping mode microcopy image of an oxide line in heightmode. (b) Phase image of the oxide line. (c) Topographical informationof the height for the oxide line.

DETAILED DESCRIPTION

The term “C₁-C_(x)-alkyl” refers to a straight, branched or cyclic alkylgroup having the designated (x) number of carbon atoms. It is understoodthat, if the group is cyclic, it must have a minimum of three carbonatoms.

The term “primary, secondary or tertiary amino” represents anR⁵R⁶N-group wherein R⁵ and R⁶, independently, represent a hydrogen,C₁-C₆ alkyl or an aryl.

The term “optionally substituted phosphino” refers to a group of theformula R⁵R⁶P— wherein R⁵ and R⁶ are as defined below.

The term “optionally substituted borane (1) and borane (2)” refers to aborane (1) or borane (2) group having one or more substituentsindependently selected from the group consisting of hydrogen, hydroxy,C₁-C₁₂ alkoxy, C₁-C₆ alkyl, thiol and aryl.

The terms “aryl” and “heteroaryl” are used as they are understood in theart. Examples of useful aryl groups are benzyl and naphthyl. Heteroarylgroups having one or more hetero-ring atoms, wherein at least oneheteroatom is nitrogen are particularly useful in the methods andcompositions of this invention. Examples of such groups include pyridyl,pyrrolyl, bipyridyl phenanthrolyl, pyrazinyl and indolyl.

The term “DNA or RNA analog” refers to a chemical analog of DNA or RNAhaving other than a phosphate linked sugar “backbone” that is capable offorming a double stranded complex with DNA or RNA.

While reference is made to silicon, it is understood that the methods ofthis invention can be applied to germanium, to produce a functionalizedgermanium surface.

The present disclosure provides a general method for covalentmodification of the surface of silicon through attachment of readilyavailable alkynes mediated by cathodic or anodic electrografting.Alkynes subjected to anodic electrografting or cathodic electrograftingin the presence of surface bound Si—H groups react with the Si—H groupsto yield surface bound alkyl or alkyne groups, respectively, as outlinedin scheme 1.

Alkynes subjected to cathodic electrografting in the presence of surfacebound Si—H groups react with the Si—H groups to yield surface boundalkyne groups according to a mechanism that was determined based on datasuch as acid quenching and infrared spectra data (see examples) and isoutlined in scheme 2.

The results of the CEG experiments suggest that the CEG reactionproceeds via a silyl anion intermediate formed by reduction of surfaceSi—H bonds in a space charge layer (see scheme 2) to yield either H. or½ H₂. The silyl anion species has been previously inferred for themechanism of alkylhalide grafting. The subsequent in situ generation ofa carbanion from deprotonation of the weakly acidic allyne leadsdirectly to nucleophilic Si—Si bond attack, as previously observed. Thesilyl anion is quenched in the presence of a proton source (0.1 M HCl indiethyl ether), leading to no incorporation of allyne. Other weaklyacidic moieties can be grafted via this CEG reaction, such as1-dodecanethiol (see FIG. 12), presumably through a similardeprotonation step and subsequent attack of Si—Si bonds by anRS-species. Minor incorporation of butyl groups (2956, 2923, and 2872cm⁻¹), which may be due to tenacious physisorption or electrochemicaldecomposition of the Bu₄NPF₆ electrolyte, is observed in all CEGreactions. The butyl groups are not removed after 30 minutes in boilingchloroform.

Alkynes subjected to anodic electrografting in the presence of surfacebound Si—H groups react with the Si—H groups to yield surface boundalkyl groups according to a mechanism that was determined based oninfrared spectra data (see examples) and is outlined in scheme 3.

In accordance with one embodiment of the present disclosure a method forforming a patterned covalently bound monolayer of organic substituentson a porous silicon substrate having a surface comprising siliconhydride groups is provided. The method comprises the steps of contactingthe surface of the porous silicon substrate with a solution or liquidcomprising an optionally substituted C₂-C₂₄ alkyne, positioning a probetip of a conductor electrode in close proximity to or in contact withthe silicon surface, using the probe tip to apply an electricalpotential sufficient to covalently bind at least a portion of the alkyneto the silicon surface, and moving the tip to create a predeterminedpattern on the porous silicon surface.

In accordance with another embodiment of the invention a method forforming a covalently bound monolayer of organic substituents on a flatSi (100), Si (111), or Ge surface is provided. The method comprises thesame steps as described in the preceding paragraph.

An electrically conductive aprotic solution optionally may be used inthe methods of the present invention. The conductive solution mayinclude any aprotic organic solvent capable of dissolving an amount ofan organic salt sufficient to enable the solution to conduct currentresponsive to a potential capable of effecting anodic or cathodicelectrografting of alkynes onto silicon surfaces. These aprotic organicsolvents may include solvents such as dioxane, dimethylformamide,dimethylacetamide, sulfolane, N-methylpyrrolidine, dimethylsulfone,dichloroethane, trichloroethane, and freons, or solvents such asdichloromethane, acetonitrile, and tetrahydrofuran. The organic salt,which when dissolved in the solvent, enables the solvent solution toconduct a current in response to application of a potential ispreferably a tertiary amine salt of a strong acid or a quaternaryammonium salt having an associated anion corresponding to a strong acid.Exemplary of such anions are tetrafluoroborate, perchlorate,perfluorosulfate, hexafluorophosphate, trifluoroacetate, and likeanions. Organic salts comprising other quarternary ammonium salts andother solvent-soluble organic salts are also applicable to theinvention. The organic salt solutions are preferably substantiallyanhydrous and substantially oxygen-free. The solutions are preferablymaintained under dry oxygen-free conditions such as that provided by aninert atmosphere, e.g., nitrogen, or a noble gas.

In carrying out the method of the present invention, an electricalcurrent is generated in a solution in contact with the silicon surface.Alternatively, the electrical current is generated more locally, bybringing a conductor electrode tip in close proximity to or in contactwith the silicon surface. The solution comprises an amount of an alkyne,as described more specifically herein below, effective to form asubstantially uniform organic monolayer on the surface of the siliconsubstrate during electrochemical deposition. A conductor electrode orelectrode tip is positioned in communication with the alkyne, and anelectrical potential is applied. The potential should be sufficient tocovalently bind at least a portion of the alkyne to the silicon surface.The conductor electrode can include any conductive material such as aplatinum, paladium, silver, gold, or graphite electrode. The duration ofthe applied potential should be sufficient to covalently bind at least aportion of the alkyne to the silicon surface.

Cathodic and anodic electrografting in accordance with the invention maybe carried out on the silicon substrate in an aprotic organic solventsolution that is substantially oxygen-free to reduce oxidation of thesubstrate that may occur under ambient conditions. A preferred method ofmaintaining a substantially oxygen-free solvent solution is to carry outthe electrochemical deposition in an inert atmosphere, e.g., in a glovebox which has been evacuated of oxygen and filled with nitrogen. It iscontemplated that other methods, normally occurring to one skilled inthe art, of creating a substantially oxygen-free environment will beapplicable to the invention.

In accordance with the method of the present invention the alkynecomprises optionally substituted C₂-C₂₄ alkynes. These alkynes mayinclude, for example, 1-pentyne, 1-dodecyne, 1,7-octadiyne,phenylacetylene, p-Br-phenylacetylene, 1,4,-diethynylbenzene,diphenylphosphino-acetylene, and 1-dodecanethiol, and any other alkynecapable of being electrografted onto a silicon substrate by anodicelectrodeposition or cathodic electrodeposition, providing alkylsubstituted and alkynyl substituted surfaces, respectively. If thealkyne is liquid, it may be provided neat. Alternatively, the alkyne maybe provided in a solution that may comprise the aprotic organic solvent.Other solutions are possible, for example a solid may be provided in1,3,5 trimethylbenzene.

The surface may be patterned with a single type of alkyne or alkylgroup, where the silicon surface is electrografted with a single type ofalkyne via CEG or AEG, respectively. Alternatively, the surface may bemade heterogeneous, consisting of different types of alkyne groups whereCEG is performed using two or more selected alkynes, or consisting ofdifferent types of alkyl groups where AEG is performed using two or moreselected alkynes. In the case of a heterogenous surface monolayer, themole fraction of the groups in the monolayer would correspond generallyto the mole fractions of the different types of alkynes in the reagentmixture used to form the monolayer. The functional groups present on anyof the alkyne reactants are preferably in a “protected” form during theelectrodeposition step and are thereafter deprotected on the surface toprovide reactive sites for further surface functionalization, i.e., forcoupling to biologically significant molecules using standard ester- oramide-forming coupling techniques. The term “protected” refers to theuse of standard protecting groups that can serve to prevent unwantedreaction of reactive functional groups during one reaction (i.e.,electrodeposition) and thereafter be removed to regenerate the reactivefunctional groups for subsequent reactions. Such protecting groups arewell-known in the art.

In another embodiment of the invention, patterns of covalently boundspecies derived from alkynes on the silicon surface can be formed bysequential photopatterning and electrografting procedures. In accordancewith this embodiment, photopatterning of alkyl and alkynyl monolayers onporous silicon surfaces is controlled by art-recognized masking anddemasking techniques. The patterned, unmasked, nonfunctionalized siliconhydride groups can be selectively reacted with a particular alkyne or amixture of alkynes using CEG or AEG.

Patterning may also be achieved using a probe tip of a conductorelectrode to “write” a pattern on the silicon surface. For example, aconducting probe atomic force microscope (CP-AFM) or scanning tunnelingmicroscope (STM) tip may be used to fabricate very fine patterns.Illustratively, the patterns may be lines about 10 molecules thick, moreparticularly about 5 molecules thick, and most particularly patterns maybe drawn comprising lines about one molecule thick. However, dependingon the application, lines of various thickness may be produced. In anillustrative embodiment, a CP-AFM tip is used under CEG conditions tocovalently attach alkynes to a silicon hydride surface, creating ananometers thick pattern of highly stable covalently bonded alkyne onsilicon.

For example, a thin layer of the alkyne would be placed on a siliconoxide wafer. The tip then would be brought into contact with the alkyneand allowed to soak for 30 seconds. The silicon oxide surface is thenreplaced with a hydride terminated silicon surface. The purpose forwetting silicon oxide with the alkyne is to avoid covering the writingsurface with obtrusive organics. This step keeps the hydride terminatedsurface as clean as possible for imaging. Then, in lateral force mode,the alkyne covered tip is then brought into contact with the hydrideterminated surface (FIG. 24). Because the reaction takes place betweenthe tip an semiconducting material, one molecule thick nanostructure canbe manufactured into well defined lines or shapes. A scheme of this canbe seen in FIGS. 25(a) and (b). Patterns such as the interdigitatedpattern of several different alkynes as shown in FIG. 25(d) may becreated by this method. While two different alkynes are illustrated inFIG. 25(d), it is understood that any number of alkynes or mixtures ofalkynes may be used, depending on the application.

In one aspect of this method, the C₂-C₂₄ alkyne is a compound of theformula:R¹—C≡C—R²

wherein

R¹ is hydrogen and R² is hydrogen, hydroxy, halo, cyano, isocyano,C₁-C₁₈ alkoxy, C₁-C₁₈ carboxy, C₁-C₁₈ alkoxycarbonyl, primary, secondaryor tertiary amino, thiol, optionally substituted phosphino, borane (1)or borane (2), or C₁-C₁₈ alkylthioether or an optionally substitutedC₁-C₁₈ alkyl, aryl, heteroaryl or vinyl group; and when R² is asubstituted group, the group is substituted with one or moresubstituents selected from the group consisting of hydroxy, halo, cyano,isocyano, C₂-C₂₄ alkynyl, C₁-C₁₈ alkoxy, C₁-C₁₈ carboxy, C₁-C₁₈alkoxycarbonyl, primary, secondary or tertiary amino, thiol, optionallysubstituted phosphino, aryl, borane (1) or borane (2), or C₁-C₁₈alkylthioether, halo C₁-C₁₈ alkyl, cyano C₁-C₁₈ alkyl, isocyano-C₁-C₁₈alkyl, C₁-C₁₈ carbamido, or C₁-C₁₈ alkylthio group, a C₁-C₁₈ ferrocenesubstituent or another electron donor, a metal chelating ligand or ametal complex thereof, or a biologically significant ligand selectedfrom an antibody, a receptor protein, DNA or RNA, or a DNA or RNA analogcapable of forming a double or triple stranded complex with DNA or RNA.

In another embodiment, any hydroxy, carboxy, amino or thiol substituentgroup is in the form of protected hydroxy, protected carboxy, protectedamino and protected thiol, respectively.

This invention further provides a patterned silicon substrate having asurface comprising one or more covalently bound monolayers wherein eachmonolayer comprises a group of the formula:R—C≡C—Si

wherein

Si is a surface silicon atom through which the substituted orunsubstituted alkynyl group is bonded to the silicon surface; and

R is hydrogen, hydroxy, halo, cyano, isocyano, C₁-C₁₈ alkoxy, C₁-C₁₈carboxy, C₁-C₁₈ alkoxycarbonyl, primary, secondary or tertiary amino,thiol, optionally substituted phosphino, borane (1) or borane (2), orC₁-C₁₈ alkylthioether or an optionally substituted C₁-C₁₈ alkyl, aryl,heteroaryl or vinyl group; and when R is a substituted group, the groupis substituted with one or more substituents selected from the groupconsisting of hydroxy, halo, cyano, isocyano, C₂-C₂₄ alkynyl, C₁-C₁₈alkoxy, C₁-C₁₈ carboxy, C₁-C₁₈ alkoxycarbonyl, primary, secondary ortertiary amino, thiol, optionally substituted phosphino, aryl, borane(1) or borane (2), or C₁-C₁₈ alkylthioether, halo C₁-C₁₈ alkyl, cyanoC₁-C₁₈ alkyl, isocyano-C₁-C₁₈ alkyl, C₁-C₁₈ carbamido, or C₁-C₁₈alkylthio group, a C₁-C₁₈ ferrocene substituent or another electrondonor, a metal chelating ligand or a metal complex thereof, or abiologically significant ligand selected from an antibody, a receptorprotein, DNA or RNA, or a DNA or RNA analog capable of forming a doubleor triple stranded complex with DNA or RNA; or R, together with thecarbon atoms to which it is attached, forms a 5-, 6-, 7- or 8-memberedring.

The invention also provides for a silicon substrate having a siliconsurface comprising one or more covalently bound monolayers, eachmonolayer comprising a group of the formula:

wherein

Si is a surface silicon atom; and

R is hydrogen, hydroxy, halo, cyano, isocyano, C₁-C₁₈ alkoxy, C₁-C₁₈carboxy, C₁-C₁₈ alkoxycarbonyl, primary, secondary or tertiary amino,thiol, optionally substituted phosphino, borane (1) or borane (2), orC₁-C₁₈ alkylthioether or an optionally substituted C₁-C₁₈ alkyl, aryl,heteroaryl or vinyl group; and when R is a substituted group, the groupis substituted with one or more substituents selected from the groupconsisting of hydroxy, halo, cyano, isocyano, C₂-C₂₄ alkynyl, C₁-C₁₈alkoxy, C₁-C₁₈ carboxy, C₁-C₁₈ alkoxycarbonyl, primary, secondary ortertiary amino, thiol, optionally substituted phosphino, aryl, borane(1) or borane (2), or C₁-C₁₈ alkylthioether, halo C₁-C₁₈ alkyl, cyanoC₁-C₁₈ alkyl, isocyano-C₁-C₁₈ alkyl, C₁-C₁₈ carbamido, or C₁-C₁₈alkylthio group, a C₁-C₁₈ ferrocene substituent or another electrondonor, a metal chelating ligand or a metal complex thereof, or abiologically significant ligand selected from an antibody, a receptorprotein, DNA or RNA, or a DNA or RNA analog capable of forming a doubleor triple stranded complex with DNA or RNA; or R together with thecarbon atoms to which it is attached, forms a 5-, 6-, 7- or 8-memberedring.

Preferred aspects of this invention are those silicon surfaces thatcontain bound alkyne groups where R² is an aryl or heteroaryl orphosphino metal chelating ligand and any metal complex of this metalchelating ligand.

Another preferred aspect of this invention are those silicon surfaceswherein at least a portion of the covalently bound R² group comprises abiologically significant ligand.

Hydrosilylation of alkynes with surface situated silicon hydride groupson a silicon surface promoted by electrografting yields a wide varietyof chemical groups covalently bound to the surface. The present methodis tolerant of alkynes substituted with functional groups such asphenyl, alkyl, and phenylphosphino groups which can be used to formcovalently bound monolayers on silicon surfaces without additionalprotecting groups.

Another advantage of this invention is that it allows formation of asurface-protecting monolayer under relatively mild conditions, i.e., atroom temperature (about 20-25° C.). Moreover, silicon having a monolayerof covalently bound organic groups demonstrates remarkable chemicalresistance. For example, when silicon functionalized with organic groupsusing this method was subjected to boiling in aqueous NaOH solution (pH10), no oxidation was seen and only minor changes in the surface IRspectra were noted. When nonfunctionalized silicon is subjected to thosesame conditions, the layer is destroyed in approximately 180 seconds.Because of the high stability displayed by silicon surfaces protected inaccordance with this invention, this methodology represents an importantstep towards the use of silicon in technologically importantapplications.

In order to illustrate the operation of this invention, the followingnon-limiting examples are provided:

EXAMPLE 1 Preparation of Porous Silicon and FT-IR and PhotoluminescenceMeasurements

FT-IR spectra. The spectra were collected using either a Perkin-Elmer2000 or a Nicolet Nexus 670 FT-IR spectrometer with a DTGS detector, intransmission mode, typically obtained at 4 cm⁻¹ resolution with 16 or 32scans collected, respectively.

Preparation of porous silicon. Porous silicon (1.12 cm²) was prepared byanodization of prime-grade n-type, P-doped, 0.65-0.95 Ω-cm silicon. Theetching was carried out with a 24% HF/24% H₂O/52% ethanol etchingsolution for 3 minutes at +76 mA cm⁻² under 25 mW cm⁻² white lightillumination. The applied current was controlled using an EG & Ginstruments, Princeton Applied Research Potentiostat/Galvanostat Model363 instrument in constant current mode. After anodization samples werewashed with ethanol and hexane before being dried under a stream ofnitrogen.

Photoluminescence measurements. PL measurements were recorded using anOriel 250W mercury arc lamp and a Bausch and Lomb monochromator set to450 nm as the excitation source. Emission was observed through a 495 nmLWP filter (GG495) with an Acton Research Spectra Pro 275 monochromator(0.275 m) and Princeton Instruments liquid N₂ cooled CCD detector (modelLN/CCD-1024-E/1).

Syntheses of 1-phenyl-2-(trimethylsilyl)acetylene and1-trimethylsilyldodecyne. Syntheses of1-phenyl-2-(trimethylsilyl)acetylene and 1-trimethylsilyldodecyne wereachieved using a method similar to that reported by C. Eaborn and D. R.M. Walton, J. Organomet. Chem., 1965, 4, 217, reaction conditions whichare directly analogous to those reported by Weber in W. P. Weber,Silicon Reagents for Organic Synthesis, Springer-Verlag, New York, 1983,p. 150.

EXAMPLE 2 Preparation of Functionalized Silicon by Electrografting

Electrografting. Electrochemical grafting is carried out in a VacuumAtomospheres Nexus One glove box filled with nitrogen. AEG and CEGcarried out on porous silicon under ambient conditions results inlarge-scale oxidation of the surface with surface oxidation appearing tobe in competition with the alkyne grafting. An ohmic contact isestablished between the backside of the porous Si sample and a sheet ofaluminum foil. A 35-40 μl aliquot of alkyne and 1 ml of 0.1 Mtetrabutylammonium hexafluorophosphate in CH₂Cl₂ are applied to theporous Si sample and a platinum loop is used as the counter electrode. Acurrent is then applied (+10 mA for AEG, −10 mA for CEG), typically for120 seconds. Afterwards, the sample is removed from the glove box, andgently washed with CH₂Cl₂/pentane and dried under a nitrogen stream. Theporous Si surfaces are then characterized by transmission mode FT-IRspectroscopy.

EXAMPLE 3 FT-IR Analysis of CEG Phenylacetylene

The same general procedures for preparation of porous silicon,electrografting, and FT-IR spectra measurements were followed as setforth in examples 1 and 2. FT-IR analysis of CEG phenylacetylene revealsSi—H_(x) stretches which are broadened and decreased in integratedintensity compared to unmodified porous silicon. The absence of aν(≡C—H) mode around 3300 cm⁻¹ and an observed sharp silylated alkyneν(C≡C) at 2159 cm⁻¹ is consistent with a Si-alkynyl surface and notsimple physisorption. For instance, the ν(C≡C) of1-phenyl-2(trimethylsilyl)-acetylene appears at 2160 cm⁻¹ while that ofphenylacetylene is observed at 2110 cm⁻¹ (see FIG. 4).

EXAMPLE 4 FT-IR Analysis OF CEG 1-Dodecyne

The same general procedures for preparation of porous silicon,electrografting, and FT-IR spectra measurements were followed as setforth in examples 1 and 2. CEG of 1-dodecyne shows a ν(C≡C) at 2176cm⁻¹, 1-trimethylsilyldodecyne at 2176 cm⁻¹, and 1-dodecyne at 2120 cm⁻¹(see FIG. 2).

EXAMPLE 5 Hydroboration OF 1-Pentynyl

The same general procedures for preparation of porous silicon,electrografting, and FT-IR spectra measurements were followed as setforth in examples 1 and 2. The 1-pentyl surface was hydroborated withBH₃.THF or a 0.5 M THF solution of disiamylborane to verify the presenceof the silylated triple bond (see FIGS. 15 and 17). The appearance of abroad band at 1580 cm⁻¹ and the concomitant consumption of the ν(C≡C) isindicative of a silylated, borylated double bond, which was verified byhydroboration of 1-trimethylsilyldodecyne and FT-IR analysis [ν(C≡C) at1584 cm⁻¹)] (see FIG. 16).

EXAMPLE 6 FT-IR OF AEG 1-Dodecyne

The same general procedures for preparation of porous silicon,electrografting, and FT-IR spectra measurements were followed as setforth in examples 1 and 2. Covalent electrografting of alkynes alsoappears to occur when an anodic potential is applied, although AEGsurfaces show complete reduction of all unsaturated bonds. The C≡Ctriple bond is not observed (˜2180 cm⁻¹), along with only a weakvibration corresponding to a hydrosilylated double bond mode (1600 cm⁻¹)in the FT-IR spectra. In contrast to CEG, AEG of 1-dodecyne has featuresrelating only to aliphatic C—H bonds (see FIG. 8).

EXAMPLE 7 FT-IR Of AEG Phenylacetylene

The same general procedures for preparation of porous silicon,electrografting, and FT-IR spectra measurements were followed as setforth in examples 1 and 2. In the spectrum of phenylacetylene AEG, ringbreathing modes at 1599 cm⁻¹, 1493 cm⁻¹, and 1446 cm⁻¹ compare closelywith polystyrene films and differ from those observed for the CEGsurface of phenylacetylene at 1596 cm⁻¹, 1489 cm⁻¹, and 1443 cm⁻¹ (seeFIGS. 4 and 9). Given the observations noted in FT-IR of the surfacesafter AEG of 1-dodecyne and 1-phenylacetylene, it is likely that asurface-initiated cationic hydrosilylation mechanism is responsible forthe Si—C bond formation in AEG reactions. Positive charges arestabilized in the depletion layer at the semiconductor-electrolyteinterface, which are attacked by alkyne monomers. This can then be thestarting point for a successive hydrosilylation or cationicpolymerization reaction.

EXAMPLE 8 Boiling of Surfaces Functionalized through AEG or CEG

The same general procedures for preparation of porous silicon,electrografting, and FT-IR spectra measurements were followed as setforth in examples 1 and 2. Boiling of the surfaces functionalizedthrough AEG for 30 minutes in CHCl₃ results in no change in FT-IR,suggesting covalent bonding as opposed to physisorption. Based on thecoincidence of the ring modes and the saturation of the C≡C bonds, weconclude that doubly hydrosilylated (bis-silylation) or possiblyoligomeric material decorates the porous silicon surface (see FIG. 11).Stability tests using boiling aqueous NaOH solution (pH 10) demonstratethe chemical resistance of AEG and CEG samples compared tounfunctionalized porous silicon. Unmodified surfaces are destroyed whenboiled in NaOH in about 180 seconds, while the CEG functionalizedsamples remain essentially unchanged after 10 minutes but for anincrease in the ν (Si—O) mode at 1050 cm⁻¹ (see FIG. 10). Extendedtreatment with ethanolic HF solution also results in no change in FT-IRspectra. The combined stability with respect to both HF and alkalinetreatment is known only for Si systems with covalently attached organiclayers.

EXAMPLE 9 Photoluminescence Spectra of CEG and AEG Samples

The same general procedures for preparation of porous silicon,electrografting, FT-IR spectra and photoluminescence measurements werefollowed as set forth in examples 1 and 2. Photoluminescence spectra ofCEG samples show varying intensities depending on the surface type (seeFIGS. 1 and 13). Upon CEG of 1-dodecyne, 1,7-octadiyne, and 1-pentynyl(see FIGS. 2-3 and 18-20) the surfaces retain between about 5 to 15% ofthe light emission, with a small red-shift of ˜10 nm relative to freshlyprepared porous silicon (λ_(max)=663 nm). The phenethynyl surface(arynyl group) and other highly conjugated alkynyl terminated surfaces(see FIGS. 5-7) show no light emission whatsoever as previouslyreported. AEG samples have more intense PL, with ˜20% remaining for thealkyl protected surface as compared to the etched hydride terminatedsurface (see FIG. 21).

EXAMPLE 10 CP-AMP Lithography

N-type phosphorus doped silicon (111) wafers (6 in. diameter:0.0011-0.0015 ohm/cm resistivity: 600-650 μm thickness) were used forall lithography experiments. As for the orientation of the crystallattice, silicon (111) was chosen for its flatness over other siliconorientations. Near atomically flat surfaces aid in reducing imagingartifacts on the surface.

Lithography was performed under ambient conditions with a DigitalInstruments Nanoscope IIIa atomic force microscope in lateral forcemode. Lateral force mode was chosen for its ability to measurefrictional forces between the probe tip and sample surface. Commerciallyavailable platinum coated silicon cantilever-tips were used fromMikro-Mash Inc. (NSC12/pt/50). All imaging was performed in tapping modeAFM using commercially available noncontact mode tips from Mikro-MashInc. A galvanostat from EG&G Instruments was used to apply constantcurrent along with an oscilloscope to measure the resulting voltage.

EXAMPLE 11 Dodecyne Line Formation

In the experimental setup for dodecyne, a constant current of 10nanoamps was used with a corresponding voltage range between 2-4 volts.Dodecyne was distilled and stored under an inert atmosphere until used.A silicon wafer was chemically oxidized in 3:1 (v:v) concentrated H₂SO₄:30% H₂O₂ (aq) at 80° C. for 60 minutes. The wafer was then etched in a5% aqueous solution of hydrofluoric acid for 5 minutes. Lateral forcemicroscopy was then used to write the organic line. The wafer was thenoptionally washed with dichloromethane, ethanol, pentane, and a rinse ofhydrofluoric acid for 10 seconds. If an oxide line were created duringthe writing process, washing with hydrofluoric acid would remove theoxide and replace it with silicon hydride.

Since a long chained alkyne was use in this case, it is expected thatdodecyne forming a covalent bond with silicon would be much “softer”than a silicon hydride bond. In tapping mode, the probe tip measures thetopography of the surface with an oscillating tip, and since dodecyne isa long alkyne it is expected that the surface would be quite elastic or“soft” when the tip comes into contact. Thus, a large degree of phasechange is expected, which is seen in FIG. 26(b). The topographicalinformation for dodecyne gives a height of one nanometer, compared tothe calculated theoretical height value of 1.848 nanometers. The reasonfor the difference in height is due to the tip pushing down on the“soft” alkyne, which distorts the shape to give a smaller actual heightvalue compared to the theoretical calculation.

EXAMPLE 12 1,4 Diethynylbenzene Line Formation

In the experimental setup for 1,4 diethynylbenzene a constant current of10 nanoamps was used. The corresponding voltage ranged between 2-3volts. Since diethynylbenzene is a solid at room temperature, a 0.1 Mconcentration was made with 1,3,5 trimethylbenzene. The solvent wasdistilled and then stored under inert conditions until use. A siliconwafer was chemically oxidized in 3:1 (v:v) concentrated H₂SO₄: 30% H₂O₂(aq) at 80° C. for 60 minutes. The wafer was then etched in a 5% aqueoussolution of hydrofluoric acid for 5 minutes. Lateral force microscopywas then used to write the organic line. The wafer was then immediatelywashed with dichloromethane, ethanol, pentane, and a rinse of a 5%aqueous solution of hydrofluoric acid for 10 seconds. Since 1,4diethynylbenzene is a hard molecule compared to dodecyne, it is expectedthat the phase change would be very small, as seen in FIG. 28(b). Thetopographical information gives a projected height of 0.5 nanometers for1,4 diethynylbenzene. The calculated theoretical height of 1,4diethynylbenzene is 0.75 nanometers. The theoretical height and themeasured height are very similar to each other, providing additionalevidence that the line is organic. As discussed above, an oxide line isruled out due to the hydrofluoric acid wash. While creation of a polymeris possible, if a polymer had been created, the height would be expectedto be much taller than it is. 1,3,5 trimethylbenzene was also used aloneto eliminate the possibility that it had covalently attached to thesurface.

EXAMPLE 13 Octadecyne Line Formation

For octadecyne a constant current of 10 nanoamps was used with acorresponding voltage range between 3-4 volts. Since octadecyne is aviscous oil at room temperature, the procedure was modified slightly. Adrop of octadecyne was placed directly on to the silicon hydride surfaceand the placed on a spin coater to create a thin layer of octadecyne.The AFM tip was then brought into contact with the organic. The tip wasthen retracted and the silicon oxide was replaced with silicon hydride.Lateral force microscopy with a scan rate of 2 microns per second wasused to write the line. The wafer was then immediately washed withdichloromethane, ethanol, pentane, and a rinse of hydrofluoric acid for10 seconds. Tapping mode AFM was used to image the height and phasecontrast. Since octadecyne has six more carbons than dodecyne, aslightly larger height difference along with a comparable phase isexpected In FIG. 28(c), the topographical height information gives aheight of 2.1 nanometers for octadecyne. The theoretical heightcalculation for octadecyne gives a value of 2.82 nanometers. FIG. 29(b)shows a noticeable phase change. Because a covalently bonded octadecynewould be much softer than the surrounding silicon hydride, this phasechange is expected. When the tip comes into contact with octadecyne thetip will push the molecule down slightly distorting the height, whichwould account for the slight deviation between the actual heightmeasurement and the theoretical calculation. Since the wafer was washedwith dichloromethane, ethanol, pentane, and hydrofluoric acid, left overoctadecyne or oxide is ruled out. Since a spin coating technique wasused to create a thin layer of octadecyne on a silicon hydride surface,an increase in the width of the line is observed.

EXAMPLE 14 Oxide Line Formation

The formation of silicon oxide lines drawn on hydride terminated siliconwafers under a negative tip bias of an atomic force microscope operatingin a ambient atmosphere has been studied in great detail. When trying towrite organic lines on the surface on silicon hydride under cathodicelectrografting conditions there are three possible outcomes, an oxide,polymer, or an alkynyl monolayer. To demonstrate that a covalentlybonded alkyne has attached a one molecule thick organic layer on asilicon surface, an oxide line was produced for comparison.

In the standard procedure for lithography of an oxide line, a siliconwafer was chemically oxidized in 3:1 (v:v) concentrated H₂SO₄: 30% H₂O₂(aq) at 80° C. for 60 minutes. The wafer was then etched in a 5% aqueoussolution of hydrofluoric acid for 5 minutes. A plastic chamber wasconstructed and placed over the AFM to obtain a humidity range between40-50%. To create an oxide line, a voltage of greater than 6 volts and asetting of 250 nanoamps is used. Lateral force microscopy was used witha writing speed of 2 microns per second to generate the line. Theresulting voltage ranged between 6-10 volts. After writing, the surfacewas dried with nitrogen to remove the excess water. To image the line,tapping mode AFM was used to produce a height and phase image of theoxide line. Taking into consideration that a phase image shows contrastcaused by differences in surface adhesion and due to the expectationthat the hardness of an oxide line would not be much different than thesurrounding silicon hydride, a very small phase change is expected.

As shown in FIG. 29(c), the height of the oxide line is approximately2.01 nanometers. The shift in the phase of the oxide line from thesurrounding hydride terminated surface is approximately 3 degrees. Theexpected height of the oxide line to be approximately 2 nanometers withthe voltage that was used. After the images were taken, the line wasrinsed with a 5% aqueous hydrofluoric acid solution for 30 seconds toremove the oxide. An image was taken again of the same region todemonstrate that the oxide line was removed.

Although the invention has been described in detail with reference tocertain preferred embodiments, variations and modifications exist withinthe scope and spirit of the invention as described and defined in thefollowing claims.

1. A method for forming a covalently bound monolayer of organicsubstituents on a silicon or germanium substrate having a surfacecomprising silicon or germanium hydride groups, said method comprisingthe steps of: contacting the surface of the substrate with a liquidcomprising an optionally substituted C₂-C₂₄ alkyne; positioning aconductor electrode tip in contact with the surface; and using theconductor electrode tip to apply an electrical potential sufficient tocovalently bind at least a portion of the alkyne to the surface.
 2. Themethod of claim 1 wherein the substrate is silicon.
 3. The method ofclaim 1 further comprising the step of moving the tip along the surfaceto create a pattern of covalently bound alkyne.
 4. The method of claim 3wherein the electrical potential is applied so that the conductorelectrode tip serves as an anode.
 5. The method of claim 4 wherein theconductor electrode tip is an atomic force microscope tip.
 6. The methodof claim 4 wherein the conductor electrode tip is a scanning tunnelingmicroscope tip.
 7. The method of claim 4 wherein the silicon substrateserves as a cathode.
 8. The method of claim 1 wherein the alkyne is acompound of the formula:R¹—C≡C—R² wherein R¹ is hydrogen and R² is hydrogen, hydroxy, halo,cyano, isocyano, C₁-C₁₈ alkoxy, C₁-C₁₈ carboxy, C₁-C₁₈ alkoxycarbonyl,primary, secondary or tertiary amino, thiol, optionally substitutedphosphino, borane (1) or borane (2), or C₁-C₁₈ alkylthioether or anoptionally substituted C₁-C₁₈ alkyl, aryl, heteroaryl or vinyl group;and when R² is a substituted group, the group is substituted with one ormore substituents selected from the group consisting of hydroxy, halo,cyano, isocyano, C₂-C₂₄ alkynyl, C₁-C₁₈ alkoxy, C₁-C₁₈ carboxy, C₁-C₁₈alkoxycarbonyl, primary, secondary or tertiary amino, thiol, optionallysubstituted phosphino, aryl, borane (1) or borane (2), or C₁-C₁₈alkylthioether, halo C₁-C₁₈ alkyl, cyano C₁-C₁₈ alkyl, isocyano-C₁-C₁₈alkyl, C₁-C₁₈ carbamido, or C₁-C₁₈ alkylthio group, a C₁-C₁₈ ferrocenesubstituent or another electron donor, a metal chelating ligand or ametal complex thereof, or a biologically significant ligand selectedfrom the group consisting of an antibody, a receptor protein, DNA orRNA, or a DNA or RNA analog capable of forming a double or triplestranded complex with DNA or RNA.
 9. The method of claim 7 wherein R²substituent is a substituted group wherein the substituent is anoptionally protected hydroxy, carboxy, amino or thiol, said methodfurther comprising the step of covalently coupling a biologicallysignificant ligand to the silicon substrate through the substituentgroup.
 10. The method of claim 7 wherein the substrate is a poroussilicon substrate.
 11. The method of claim 7 wherein the substrate is aflat silicon substrate.
 12. The method of claim 7 wherein the substrateis germanium.